[gmx-users] Bootstrapping using g_wham

[Jochen Hub]

Hi,

sorry for this late comment, I just stepped over this thread.

Bootstrapping is indeed slow, because a complete WHAM analysis must be 
done for each bootstrap. I usually do much less bootstraps (around 50 to 
100 gives a reasonable estimate), less bins, and I sometimes I reduce 
the tolerance for convergence. I would first play a bit with the 
tolerance and bins to see if they change your profile, probably they do 
not. Then you can use, e.g.

-nBootstrap 100 -bins 200 -tol 1e-5

Cheers,
Jochen


Am 6/15/12 1:19 PM, schrieb Tsjerk Wassenaar:
> Hey,
>
> Most statistics texts on bootstrapping will advise taking in the order
> of a thousand bootstrap samples. Don't know about the number of bins,
> but in any case, the problem shouldn't be that hard computationally.
> Have you checked the process? Is it really still running, has it
> stalled? And how long does one bootstrap sample take to process?
> Always good to check one before running a thousand...
>
> Cheers,
>
> Tsjerk
>
> On Fri, Jun 15, 2012 at 12:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 6/14/12 5:51 PM, rainy908 wrote:
>>>
>>> Hi,
>>>
>>> I am currently using bootstrapping in g_wham to estimate the uncertainty
>>> in my PMF.  I use a number of 1000 bootstraps.
>>>
>>> /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \
>>>   -ip gwham.dat \
>>>   -bins 5000 \
>>>   -hist histo.xvg \
>>>   -bsres bsResult.xvg \
>>>   -nBootstrap 1000
>>>
>>> This process has been running on 1 node for the past 4 days straight, and
>>> I am not sure when it will ever finish.  Should I be concerned?
>>>
>>
>> I certainly would be.  You're using a very large number of bins and
>> bootstraps, far above the default value of 200 for each.  Do you need that
>> many?  What happens if you run with values of 200 of -bins and -nBootstrap?
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
>>
>>
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-- 
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------